Normal Mode Dynamics Comparison of Proteins

Abstract

Sequence and structure comparisons are fundamental techniques that enable exploration of the sequence and structural spaces of proteins. Homology detection, function prediction, and protein classification rely on these techniques. However, protein structures are dynamic, rather than static, and such protein dynamics play a key role in a wide range of biological activities. Therefore, protein dynamics comparison algorithms may shed light on the relationship between proteins′ dynamics and function. Here, we review different strategies for comparing dynamics of proteins. Special emphasis is given to newly developed algorithms that compare dynamics of proteins with no apparent sequence or structural similarity and to the qualitative differences between these algorithms.